OutriderDataSet-class {OUTRIDER} | R Documentation

## OutriderDataSet class and constructors

### Description

The OutriderDataSet class is designed to store the whole OUTRIDER data set needed for an analysis. It is a subclass of `RangedSummarizedExperiment`. All calculated values and results are stored as assays or as annotation in the mcols structure provided by the `RangedSummarizedExperiment` class.

### Usage

    OutriderDataSet(se, countData, colData, ...)

### Arguments

`se` | A RangedSummarizedExperiment object or any object which inherits from it and contains a count matrix as the first element in the assay list.
`countData` | A simple count matrix. If dim names are provided, they have to be unique. This is only used if no `se` object is provided.
`colData` | Additional to the count data a `DataFrame` can be provided to annotate the samples.
`...` | Further arguments can be passed to `DESeqDataSet`, which is used to parse the user input and create the initial `RangedSummarizedExperiment` object.

### Value

An OutriderDataSet object.

### Author(s)

Christian Mertes mertes@in.tum.de, Felix Brechtmann brechtma@in.tum.de

### Examples

    ods <- makeExampleOutriderDataSet()
    ods

    ods <- makeExampleOutriderDataSet(dataset="Kremer")
    ods

[Package OUTRIDER version 1.6.0 Index]